stamppGmatrix {StAMPP}

Genomic Relationship Calculation

Description

This function calculates a genomic relationship matrix following the method decribed by Yang et al (2010)

Usage

stamppGmatrix(geno)

Arguments

geno

a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels

Value

An object of class matrix which contains the genomic relationship values between each individual

Author(s)

Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>

References

Yang J, Benyamin B, McEvoy BP, et al (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42, 565-569. <doi:10.1038/ng.608>

Examples

# import genotype data and convert to allele frequecies
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")
# Calculate genomic relationship values between each individual
potato.fst <- stamppGmatrix(potato.freq)